k-mer count random forest
Random forest whose input is a fixed-length vector of the sequence's 3-mer or 4-mer counts, with no reading-frame information, trained on the same MPRA training set as FramePool50.
Overview
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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
4 evaluations · 4 results. Different protocols are not a single leaderboard.
Sorted by Pearson (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
All 4 result rows with coverage, uncertainty and sources
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: 3mer_random_forest | Protocol: FramePool study MRL: Random 25-100nt Dataset subset: Sample MPRA Random 25-100nt | 0.616 Pearson unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and source3mer_random_forest random-25-100nt Not reported Aggregation: Not reported FramePool 2021 primary article; FramePool Supplementary Table S4 · S4 Table cell C2; row 3mer_random_forest; S7–S8 MPRA correlation plots |
| Configuration: 4mer_random_forest | Protocol: FramePool study MRL: Random 25-100nt Dataset subset: Sample MPRA Random 25-100nt | 0.647 Pearson unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and source4mer_random_forest random-25-100nt Not reported Aggregation: Not reported FramePool 2021 primary article; FramePool Supplementary Table S4 · S4 Table cell C3; row 4mer_random_forest; S7–S8 MPRA correlation plots |
| Configuration: 3mer_random_forest | Protocol: FramePool study MRL: Random 50nt Dataset subset: Sample MPRA Random 50nt | 0.732 Pearson unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and source3mer_random_forest random-50nt Not reported Aggregation: Not reported FramePool 2021 primary article; FramePool Supplementary Table S4 · S4 Table cell B2; row 3mer_random_forest; S7–S8 MPRA correlation plots |
| Configuration: 4mer_random_forest | Protocol: FramePool study MRL: Random 50nt Dataset subset: Sample MPRA Random 50nt | 0.75 Pearson unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and source4mer_random_forest random-50nt Not reported Aggregation: Not reported FramePool 2021 primary article; FramePool Supplementary Table S4 · S4 Table cell B3; row 4mer_random_forest; S7–S8 MPRA correlation plots |
Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.
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How it works, versions and access
Versions and evaluated configurations
- 3mer_random_forest · configuration of
- 4mer_random_forest · configuration of
Evidence
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Evidence table
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2 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Description Random forest whose input is a fixed-length vector of the sequence's 3-mer or 4-mer counts, with no reading-frame information, trained on the same MPRA training set as FramePool50. Individual claims | FramePool 2021 primary article uc20260930-source-framepool-2021: Methods, Random forest models ('random forest models which use k-mer counts as input features ... 3mer_random_forest and 4mer_random_forest'); S7 Fig caption ('offers no frame information') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2021 journal article XML; PMC8136849.1 | source checked ["automated-source-review","ai-assisted-source-review"] · 2026-10-11 Audit detailsApproved. Checked the 10 method and model descriptions against their sources (EVmutation, GEMME and RSALOR abstracts, the FramePool k-mer random forests, the RhoMax BLASSO text) and spot-checked the 49 mRNABench rows against Appendix A; all accurate. Licences on the 3 new sources match their Europe PMC records. At the reviewer's suggestion, the en dash printed in some checkpoint names is written as a hyphen in the descriptions. Field: Claim: metadata-correction-07fcb29b42cc73bc0f97 Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Description Random forest whose input is a fixed-length vector of the sequence's 3-mer or 4-mer counts, with no reading-frame information, trained on the same MPRA training set as FramePool50. Individual claims | FramePool Supplementary Table S4 uc20260930-source-framepool-2021: Methods, Random forest models ('random forest models which use k-mer counts as input features ... 3mer_random_forest and 4mer_random_forest'); S7 Fig caption ('offers no frame information') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2021 published S4 XLSX | source checked ["automated-source-review","ai-assisted-source-review"] · 2026-10-11 Audit detailsApproved. Checked the 10 method and model descriptions against their sources (EVmutation, GEMME and RSALOR abstracts, the FramePool k-mer random forests, the RhoMax BLASSO text) and spot-checked the 49 mRNABench rows against Appendix A; all accurate. Licences on the 3 new sources match their Europe PMC records. At the reviewer's suggestion, the en dash printed in some checkpoint names is written as a hyphen in the descriptions. Field: Claim: metadata-correction-07fcb29b42cc73bc0f97 Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
2 source records and release history
- FramePool 2021 primary article · Original source · 2021 journal article XML; PMC8136849.1
- FramePool Supplementary Table S4 · Original source · 2021 published S4 XLSX
Technical metadata and extraction receipts
Stable ID: uc20260930-method-k-mer-count-random-forest
- areas
- rna-transcriptomes
- source locator
- S1/S4 Table; Methods Framepool model and Model training; S7–S8 figure captions
- review
- method: automated-source-review; reviewer: codex; reviewed at: 2026-09-30T21:40:59.576893+00:00; scope: Primary-source transcription and catalogue applicability audit; not human scientific review or independent experimental reproduction.; reviewer note: role: experimental use-case curation
- entity level
- method
- identity scope
- Family/method identity only; no undocumented checkpoint equivalence.
Related records
- subject: k-mer count random forest: description
- configuration of: 3mer_random_forest
- configuration of: 4mer_random_forest